OBJECTIVES: Analyze the economic impact of the A-H1N1 flu epidemic for the health sector in Mexico in the 2009-2010 period, that resulted in the first pandemic of the XXI century, in order to plan the resources provision and review policies aimed to deal with similar future events. METHODS: The exercise had several stages. First, a collect of the expenditures incurred by the health sector at federal level between April 2009 and August 2010 was made. Second, the collected information was classified into two areas of analysis: a) health care expenditures, and b) additional costs from purchasing and application of vaccines, medical equipment, drugs and health products, federal support to states, and national media campaigns. Third, health care expenditure and expenditure by area of analysis was estimated by aggregating all costs. RESULTS: Total federal expenditure related to addressing the epidemic in the health sector was estimated in USD$ 733.3 million, 32% linked to health care and 93.7% exercised in 2009, corresponding to 11.2% of the total health expenditure budget for this year. This expenditure involved medical attention of 368 thousands patients, purchasing and application of 6.8 million of anti-flu seasonal vaccines and 30 million of anti-AH1N1flu vaccines. For health care, a total expenditure of USD$ 216.7 million was estimated, 80% exercised in 2009, that involves medical attention of 330 thousand patients. A total expenditure of USD$ 516.3 million was estimated for additional costs, more than 99% exercised in 2009. The main component of this area was the purchase and application of A-H1N1 flu vaccine (USD$ 228.8 million). CONCLUSIONS: The exercise allows knowing the mayor spending areas and generates evidence to strengthen the financial and operational planning processes to face similar health events, such as the need to anticipate resources and contingency funds in addition to administrative and operational processes.